[Chimera-users] move a structure into another one

[Elaine Meng]

Dear Francesco,
Chimera does not have any option to create a lipid bilayer.  If you 
have a bilayer structure already, open as a different model, you can 
move the protein and bilayer individually by activating/deactivating 
them for motion.   Then you would have to delete lipid molecules that 
overlap the protein manually before saving to a file.  In other words, 
there is no automatic embedding of a structure in a membrane or a 
solvent box.

about activating/deactivating for motion:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef

about writing a PDB file:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb

Note even if you save to a single file, the models will still be 
treated as separate models.  You would still have to manually edit the 
file to get everything into one model, avoiding use of duplicate atom 
numbers, etc.

Best
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html


On Nov 18, 2007, at 8:26 AM, Francesco Pietra wrote:

> I have installed chimera-1.2470 on Debian Linux i386. Thank you.
> I want to insert a protein into a lipid membrane in a precise 
> opientation, then
> save the protein pdb in this configuration.
> I used VMD in the last few days to this redard. I wonder whether I can 
> stick to
> Chimera for this purpose too. I tried by selecting "protein", though 
> it was
> difficult to proceed.
> Thanks
> francesco pietra